Comments on: 5 structural search engines – who are your protein’s neighbors? http://rosettadesigngroup.com/blog/289/5-structural-search-engines/ Trading tips and news on modeling proteins, DNA, RNA, small molecules, folding, docking, design..... Sat, 28 Jan 2012 16:25:00 +0000 hourly 1 http://wordpress.org/?v=3.0 By: Peter Vanhee http://rosettadesigngroup.com/blog/289/5-structural-search-engines/comment-page-1/#comment-7680 Peter Vanhee Sat, 22 Aug 2009 17:34:42 +0000 http://rosettadesigngroup.com/blog/?p=289#comment-7680 Another very useful tool for structural alignment is Mustang from Arun S. Konagurthu et al.: http://www.bx.psu.edu/arun/research/mustang If you would like to combine sequence with structural alignment, I would certainly recommend Expresso (part of the T-Coffee suite developed by the lab of Cedric Notredame). A webserver is implemented at http://www.tcoffee.org/ Another very useful tool for structural alignment is Mustang from Arun S. Konagurthu et al.:

http://www.bx.psu.edu/arun/research/mustang

If you would like to combine sequence with structural alignment, I would certainly recommend Expresso (part of the T-Coffee suite developed by the lab of Cedric Notredame). A webserver is implemented at

http://www.tcoffee.org/

]]> By: Emre Guney http://rosettadesigngroup.com/blog/289/5-structural-search-engines/comment-page-1/#comment-4045 Emre Guney Sun, 26 Apr 2009 10:40:37 +0000 http://rosettadesigngroup.com/blog/?p=289#comment-4045 Several structural comparison methods inheriting geometric hashing paradigm to recognize common substructures of given structures exist. http://bioinfo3d.cs.tau.ac.il/servers.html The algorithm works in the following way: Each point (corresponding to the positions of Calpha atoms) of a structure is redefined with respect to coordinate bases of all possible non-collinear point triplets in the structure to be able to define the object invariant to rigid transformation (rotation and translation). Then redefined points are inserted into a hash table where redefined point is the key of hash table entry and the basis with respect to which the point is defined and identifier of the structure pair is the value of that hash table entry. Once such a hash table is constructed with available structures a new structure can be searched for similarities with existing structures in the hash table. Points of the new structure is redefined as in the first step of the hash table construction and then the hash table is queried with the redefined points and matching basis set and structure identifier pair is cast a vote. Whichever structure (or subset of the structure) gets the most vote when votes are grouped with respect to basis sets, is concluded to be structurally similar to the given structure. Several structural comparison methods inheriting geometric hashing paradigm to recognize common substructures of given structures exist.

http://bioinfo3d.cs.tau.ac.il/servers.html

The algorithm works in the following way:
Each point (corresponding to the positions of Calpha atoms) of a structure is redefined with respect to coordinate bases of all possible non-collinear point triplets in the structure to be able to define the object invariant to rigid transformation (rotation and translation). Then redefined points are inserted into a hash table where redefined point is the key of hash table entry and the basis with respect to which the point is defined and identifier of the structure pair is the value of that hash table entry. Once such a hash table is constructed with available structures a new structure can be searched for similarities with existing structures in the hash table. Points of the new structure is redefined as in the first step of the hash table construction and then the hash table is queried with the redefined points and matching basis set and structure identifier pair is cast a vote. Whichever structure (or subset of the structure) gets the most vote when votes are grouped with respect to basis sets, is concluded to be structurally similar to the given structure.

]]> By: Iddo Friedberg http://rosettadesigngroup.com/blog/289/5-structural-search-engines/comment-page-1/#comment-2948 Iddo Friedberg Mon, 23 Mar 2009 21:12:07 +0000 http://rosettadesigngroup.com/blog/?p=289#comment-2948 FATCAT http://fatcat.burnham.org/ Protein structures are flexible and undergo structural rearrangements as part of their function. FATCAT (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists) is an approach for flexible protein structure comparison. It simultaneously addresses the two major goals of flexible structure alignment; optimizing the alignment and minimizing the number of rigid-body movements (twists) around pivot points (hinges) introduced in the reference structure. In FATCAT, the structure alignment is formulated as the AFPs (aligned fragment pairs) chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0. Dynamic programming is used to find the optimal chaining. FATCAT http://fatcat.burnham.org/

Protein structures are flexible and undergo structural rearrangements as part of their function. FATCAT (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists) is an approach for flexible protein structure comparison. It simultaneously addresses the two major goals of flexible structure alignment; optimizing the alignment and minimizing the number of rigid-body movements (twists) around pivot points (hinges) introduced in the reference structure. In FATCAT, the structure alignment is formulated as the AFPs (aligned fragment pairs) chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0. Dynamic programming is used to find the optimal chaining.

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